Monte Carlo and molecular dynamics

Berne B J 1985 Molecular dynamics and Monte Carlo simulations of rare events Multiple Timescales ed J V Brackbill and B I Cohen (New York Academic Press)... 

A comprehensive and up-to-date introduction to the ideas of molecular dynamics and Monte Carlo, with statistical mechanical background, advanced teclmiques and case studies, supported by a Web page for software download. 

The most important molecular interactions of all are those that take place in liquid water. For many years, chemists have worked to model liquid water, using molecular dynamics and Monte Carlo simulations. Until relatively recently, however, all such work was done using effective potentials [4T], designed to reproduce the condensed-phase properties but with no serious claim to represent the tme interactions between a pair of water molecules. 

M. Jalaie, K. B. Lipkowitz, Published force field parameters for molecular mechanics, molecular dynamics, and Monte Carlo simulations, in Reviews in Computational Chemistry, Vol. 14, K.B. Lipkowitz, D. B. Boyd (Eds.), Wiley-VCH, New York, 2000, pp. 441-486. 

Differences Between the Molecular Dynamics and Monte Carlo Methods... 

Calculations of relative partition coefficients have been reported using the free energy perturbation method with the molecular dynamics and Monte Carlo simulation methods. For example, Essex, Reynolds and Richards calculated the difference in partition coefficients of methanol and ethanol partitioned between water and carbon tetrachloride with molecular dynamics sampling [Essex et al. 1989]. The results agreed remarkably well with experiment... 

Recently, molecular dynamics and Monte Carlo calculations with quantum mechanical energy computation methods have begun to appear in the literature. These are probably some of the most computationally intensive simulations being done in the world at this time. 

Molecular dynamics and Monte Carlo simulations can be used, but these methods involve very complex calculations. They are generally only done when more information than just the boiling point is desired and they are not calculations for a novice. 

Mesoscale simulations model a material as a collection of units, called beads. Each bead might represent a substructure, molecule, monomer, micelle, micro-crystalline domain, solid particle, or an arbitrary region of a fluid. Multiple beads might be connected, typically by a harmonic potential, in order to model a polymer. A simulation is then conducted in which there is an interaction potential between beads and sometimes dynamical equations of motion. This is very hard to do with extremely large molecular dynamics calculations because they would have to be very accurate to correctly reflect the small free energy differences between microstates. There are algorithms for determining an appropriate bead size from molecular dynamics and Monte Carlo simulations. 

Molecular Dynamics and Monte Carlo Simulations. At the heart of the method of molecular dynamics is a simulation model consisting of potential energy functions, or force fields. Molecular dynamics calculations represent a deterministic method, ie, one based on the assumption that atoms move according to laws of Newtonian mechanics. Molecular dynamics simulations can be performed for short time-periods, eg, 50—100 picoseconds, to examine localized very high frequency motions, such as bond length distortions, or, over much longer periods of time, eg, 500—2000 ps, in order to derive equiUbrium properties. It is worthwhile to summarize what properties researchers can expect to evaluate by performing molecular simulations ... 

Various equations of state have been developed to treat association ia supercritical fluids. Two of the most often used are the statistical association fluid theory (SAET) (60,61) and the lattice fluid hydrogen bonding model (LEHB) (62). These models iaclude parameters that describe the enthalpy and entropy of association. The most detailed description of association ia supercritical water has been obtained usiag molecular dynamics and Monte Carlo computer simulations (63), but this requires much larger amounts of computer time (64—66). 

In the second group come molecular dynamics and Monte Carlo simulations, especially those where the solvent is modelled without being explicitly included. Their fourth class is the related supermolecule class, where we actually include solvent molecules in the simulation, and treat the entire array of molecules according to the rules of quantum mechanics or whatever. 

Eds Ciccotti G., Frenkel D., McDonald I. R.) Simulation of Liquids and Solids Molecular Dynamics and Monte Carlo Methods in Statistical Mechanics (North-Holland Physics Publishing, Amsterdam) (1987). 

Chemistry, like other sciences, progresses through the use of models. Models are the means by which we attempt to understand nature. In this book, we are primarily concerned with models of complex systems, those systems whose behaviors result from the many interactions of a large number of ingredients. In this context, two powerful approaches have been developed in recent years for chemical investigations molecular dynamics and Monte Carlo calculations [4-7]. Both techniques have been made possible by the development of extremely powerful, modern, high-speed computers. 

Molecular dynamics and Monte Carlo simulations have been extensively applied to molten salts since 1968 to study structure, thermodynamic properties, and dynamic properties from a microscopic viewpoint. Several review papers have been published on computer simulation of molten salts. " Since the Monte Carlo method cannot yield dynamic properties, MD methods have been used to calculate dynamic properties. 

Biirgi R, Kollman PA, van Gunsteren WF (2002) Simulating proteins at constant pH An approach combining molecular dynamics and Monte Carlo simulation. Proteins 47 469-480. 

---